I have the homebrew channel, but dont really want it anymore
1) How do I remove it ?
2) If I remove it, and upgrade to 3.3E will my wiikey still play same region backups e.g. wii music

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do it the easy way, delete channel through data management, don't be worried, nothing is going to cause issues with your wii if you were to update, and deffinately cannot cause problems to your modchip!